have you taken a really close look at the sizes in the directions? I have had the same problem, and after my second attempt at making a block resulted in still being too small, I found my calculator. Sometimes in the writing and editing process, if they make a change to one piece, that change doesn't get updated everywhere that it should. If the directions say to cut a 4" square, we know that it will finish at a 3-1/2" square. But maybe the directions say it will finish at 3-3/4"? check that. Another couple thoughts - have you checked your pressing? Have you tried sewing 'scant' 1/4" seams? (just 2 threads short of a 1/4")
hope this helps